This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Mass spectrometry is a powerful experimental tool that can contribute significantly to the annotation of completed genomes. The generation of high-throughput proteomic data from an organism can confirm protein coding genes predicted by computational methods;yet, have not been validated using orthogonal mRNA-based approaches. In addition, shotgun proteomic technology can provide experimental confirmation for small open reading frames (ORFs) that are difficult to impossible to identify computationally. We describe a general mass spectrometry based approach for gene annotation of any organism at the metazoan level of complexity and demonstrate the effectiveness of this process using the nematode C. elegans.